MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iMM904 [2].
Target metabolite : cdp_n
List of minimal gene deletion strategies (Download)

Gene deletion strategy (148 of 174: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: YDL168W YMR303C YBR068C YDR046C YBR069C YGR087C YLR044C YLR134W YDR380W YDL080C YKL192C YPL148C YBR291C YJL060W YCL025C YKR039W YOL020W YOR120W YOL059W YGR191W YDR403W YJL121C YLR348C YPR069C YBR176W YML120C YEL046C YFR047C   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.109303 (mmol/gDw/h)
  Minimum Production Rate : 0.118819 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 10.000000
  EX_o2_e : 2.000000
  EX_nh4_e : 1.000051
  EX_pi_e : 0.271773
  EX_so4_e : 0.008449

Product: (mmol/gDw/h)
  EX_h_e : 22.449965
  EX_h2o_e : 13.695526
  EX_succ_e : 7.034489
  EX_3c3hmp_e : 3.355616
  EX_pyr_e : 0.596206
  EX_3mop_e : 0.253639
  Auxiliary production reaction : 0.118819
  EX_pap_e : 0.006263
  EX_gly_e : 0.000567
  EX_for_e : 0.000565

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 27-Sep-2023
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